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2020-05-14Workflow fixesPeter Amstutz
2020-05-13Update paper.mdLLTommy
2020-05-13Adding some more labels and adjusting some querieslltommy
2020-05-12Virtuoso uploader: does not delete graph yetPjotr Prins
2020-05-12Update graph scriptPjotr Prins
2020-05-12Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-05-11Merge pull request #49 from mr-c/add_pangenome_browser_prepPeter Amstutz
add pangenome browser prep
2020-05-06Adding additional frontend option (PATO_0001340) to QClltommy
2020-05-06Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-05-06Merge pull request #50 from adamnovak/upload-listsPjotr Prins
Add support for lists in the web uploader
2020-05-06Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-05-05Add back necessary form-swapping javascriptAdam Novak
This partially reverts 03cbed808805ccdbff639eaa67e8f8b26c7275b3. Unless we actually take the inactive form fields out of the form in the DOM, their "required" attributes will prevent form submission. We can't just hide them.
2020-05-05Use invisible class instead of hidden classAdam Novak
2020-05-05Add JS at front end for lists, and date support on backendAdam Novak
2020-05-05Handle doubles and lists on the backendAdam Novak
2020-05-05preserve the directory layout of segmentation.pyMichael R. Crusoe
2020-05-05move some tools into the shared repoMichael R. Crusoe
2020-05-04Sort input to hopefully get container reusePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04bump jerven/spodgi image to 0.0.6Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04Remove debug flag from workflow submitPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-04add pangenome browser prepMichael R. Crusoe
2020-05-04Increase RAM for minimap2Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-03Set a RAM requirement on odgi_to_rdf to influence it to run on c5Peter Amstutz
(because on a t3 it takes forever) Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-05-01Set verison tag on spodgi container imagePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Merge pull request #47 from AndreaGuarracino/patch-15Peter Amstutz
fixed UO_0000036 for year
2020-04-30fixed UO_0000036 for yearAndrea Guarracino
2020-04-30Add py-dateutil to dependencies.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Handle running in a container with no usernamePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Last addition/edits to the meta data schemalltommy
2020-04-30Merge pull request #41 from AndreaGuarracino/patch-14LLTommy
the date is now handled more formally (YYYY-MM-DD)
2020-04-30Import script fixesPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Wrap import script to run as a workflowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29Fix description content type for PyPiPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29Use subprocess invocation is backwards compatible with Python 3.5Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29Add referencePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29the date is now handled more formallyAndrea Guarracino
all the date are saved as "YYYY-MM-DD"
2020-04-29fixing JS due to name changes so the demo works againlltommy
2020-04-29Reverting country list back, something went wrong therelltommy
2020-04-29Merge pull request #40 from AndreaGuarracino/patch-13LLTommy
updated the script to manage list field, and added new terms into the dicts
2020-04-28updated to manage list fields and added new control on nasopharyngeal/throat ↵Andrea Guarracino
swab
2020-04-28Updated with new termsAndrea Guarracino
2020-04-28Updated with new termsAndrea Guarracino
2020-04-28Updated - 1731 IDs - 2020/04/28Andrea Guarracino
2020-04-28Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-28Decision to settle for float instead of integers for the coveragelltommy
2020-04-28Update spodgi docker imagePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-28Call clustalw to compare sequence to referencePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-28Whatever happend to the minimal metadata, I restored itlltommy
2020-04-28Adding field 'publication' to the maximum examplelltommy
2020-04-28Changes to the structure - we use lists now instead of strings where it ↵lltommy
makes sense. This allows us to have multiple values where in makes sense
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